Intelligent membranes with adaptive gating channels play a crucial role in cellular functions and separation processes. This study introduces a novel approach to controlling channel expansion using biomimetic adaptive aggregates, fundamentally overcoming the drawbacks of existing methods relying on intertwined polyelectrolyte chains for channel blockage. Specifically, a pH‐responsive 2D material membrane is constructed through the self‐assembling of protein‐mimetic zwitterionic polydopamine (ZPDA) soft molecular aggregates within graphene oxide (GO) interlayers. Similar to the conformational switch of inserted proteins in cellular membranes, the embedded ZPDA in GO nanofluidic channels undergoes an adaptive conformational transformation in response to pH changes. This dynamic adjustment of ZPDA physicochemical properties allows for reversible regulation of GO nanofluidic channel size and charge by external pH modulation. The resulting GO/ZPDA membrane exhibits programmable separation performance for dye molecules (i.e., water permeance of 18.8–35.4 L m−2 h−1 bar−1 and molecular selectivity of 73.7–32.9) and salt ions (i.e., ionic permeance of 0.69–1.25 mol m−2 h−1 and ionic selectivity of 20.8–21.9). This work sheds new light on the engineering of intelligent stimuli‐responsive 2D nanofluidic channels with adaptive gating properties, holding promise across a wide range of applications including separation, drug delivery, sensing, and catalysis.